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mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice

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Abstract

Purpose

The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of EDNRBm1yzcm and wild mice.

Methods

RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed.

Results

This study identified 8354 differentially expressed genes in EDNRBm1yzcm and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When P < 0.05, 1081 GO terms and 320 KEGG pathways reached a significant level. Finally, through the existing studies and the enrichment results of differentially expressed genes, it was determined that axon guidance and the focal adhesion pathway may be closely related to the occurrence of HSCR.

Conclusions

This study analyzed and identified the differential genes in colonic tissues between EDNRBm1yzcm mice and wild mice, which provided new insight for further mining the potential pathogenic genes of Hirschsprung’s disease.

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Data availability

The datasets generated from this study were submitted to National Genomics Data Center (NGDC) with accession code: PRJNA1003694.

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Acknowledgements

The authors thank Dr. Chen Bing of Yangzhou University to donate EDNRBm1yzcm mice.

Funding

This research was funded by the National Natural Science Foundation of China, grant number 81770514. The funding bodies had no role in the design of the study and collection, analysis, and interpretation of data or in writing the manuscript.

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Authors and Affiliations

  1. Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi Province, China

    Qiwen Yang, Fuwen Wang, Zhaofei Wang, Jiajun Guo, Tingjin Chang, Baligen Dalielihan, Ge Yang, Chuzhao Lei & Ruihua Dang

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  1. Qiwen Yang
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  2. Fuwen Wang
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  3. Zhaofei Wang
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Contributions

RHD was involved in conceptualization, project administration, and funding acquisition. QWY, FWW, and ZFW were involved in methodology, data curation, and visualization. JJG was responsible for software and resources. TJC did validation. LGB performed formal analysis. GY performed investigation. QWY contributed to writing––original draft preparation. CZL contributed to writing––review and editing. All the authors have read and agreed to the published version of the manuscript.

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Correspondence to Ruihua Dang.

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Yang, Q., Wang, F., Wang, Z. et al. mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice. Pediatr Surg Int 39, 268 (2023). https://doi.org/10.1007/s00383-023-05544-5

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